Human Gene CLEC4A (uc001qtz.1) Description and Page Index
  Description: Homo sapiens C-type lectin domain family 4, member A (CLEC4A), transcript variant 1, mRNA.
RefSeq Summary (NM_016184): This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:8,276,228-8,291,203 Size: 14,976 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr12:8,276,475-8,290,883 Size: 14,409 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:8,276,228-8,291,203)mRNA (may differ from genome)Protein (237 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: CLC4A_HUMAN
DESCRIPTION: RecName: Full=C-type lectin domain family 4 member A; AltName: Full=C-type lectin DDB27; AltName: Full=C-type lectin superfamily member 6; AltName: Full=Dendritic cell immunoreceptor; AltName: Full=Lectin-like immunoreceptor;
FUNCTION: May be involved in regulating immune reactivity. May play a role in modulating dendritic cells (DC) differentiation and/or maturation. May be involved via its ITIM motif (immunoreceptor tyrosine-based inhibitory motifs) in the inhibition of B-cell-receptor-mediated calcium mobilization and protein tyrosine phosphorylation.
SUBUNIT: May interact with PTPN6 via its ITIM motif.
SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein (Probable).
TISSUE SPECIFICITY: Expressed in dendritic cells, myeloid cells, B-cells and HL-60 cells (at protein level). TNF alpha, IL-1 alpha, and LPS, down-regulated expression at the surface of neutrophils (at protein level). Expressed preferentially in hematopoietic tissues. Expressed in peripheral blood leukocytes, neutrophils, moderate quantities in spleen, lymph node, and bone marrow, and at very low levels in thymus. Expressed in Ag-presenting cells (DC, monocytes, macrophages and B-cells), as well as on granulocytes. Expression was decreased in DC by signals inducing its maturation (e.g. CD40 ligand, LPS, and TNF alpha).
INDUCTION: Isoform 2 mRNA expression is up-regulated by agonists of neutrophils CSF2/GM-CSF, IL3/interleukin-3, IL4/interleukin-4 and IL13/interleukin-13.
DOMAIN: Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2- containing phosphatases.
SIMILARITY: Contains 1 C-type lectin domain.
SEQUENCE CAUTION: Sequence=AAL56016.1; Type=Frameshift; Positions=229;
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=DCIR; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_00137";

-  MalaCards Disease Associations
  MalaCards Gene Search: CLEC4A
Diseases sorted by gene-association score: inflammatory bowel disease 6 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.31 RPKM in Whole Blood
Total median expression: 61.94 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -71.30247-0.289 Picture PostScript Text
3' UTR -81.10320-0.253 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold

Pfam Domains:
PF00059 - Lectin C-type domain

SCOP Domains:
56436 - C-type lectin-like

ModBase Predicted Comparative 3D Structure on Q9UMR7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0030246 carbohydrate binding

Biological Process:
GO:0002223 stimulatory C-type lectin receptor signaling pathway
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0007155 cell adhesion
GO:0007166 cell surface receptor signaling pathway
GO:0045087 innate immune response

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF067800 - Homo sapiens HDCGC13P mRNA, complete cds.
AJ133532 - Homo sapiens mRNA for dendritic cell immunoreceptor.
AF328684 - Homo sapiens Fc-epsilon receptor III mRNA, complete cds.
BC117439 - Homo sapiens C-type lectin domain family 4, member A, mRNA (cDNA clone MGC:151048 IMAGE:40125990), complete cds.
BC117441 - Homo sapiens C-type lectin domain family 4, member A, mRNA (cDNA clone MGC:151050 IMAGE:40125992), complete cds.
AF109146 - Homo sapiens C-type lectin superfamily 6 (CLECSF6) mRNA, complete cds.
BC074822 - Homo sapiens C-type lectin domain family 4, member A, mRNA (cDNA clone MGC:103930 IMAGE:30915322), complete cds.
BC074874 - Homo sapiens C-type lectin domain family 4, member A, mRNA (cDNA clone MGC:104026 IMAGE:30915470), complete cds.
HQ258754 - Synthetic construct Homo sapiens clone IMAGE:100072784 C-type lectin domain family 4, member A (CLEC4A) gene, encodes complete protein.
KJ893764 - Synthetic construct Homo sapiens clone ccsbBroadEn_03158 CLEC4A gene, encodes complete protein.
KJ898795 - Synthetic construct Homo sapiens clone ccsbBroadEn_08189 CLEC4A gene, encodes complete protein.
AF200738 - Homo sapiens C-type lectin DDB27 short form (DDB27) mRNA, complete cds.
EU196761 - Homo sapiens C-type lectin domain family 4 member A transcript variant 5 (CLEC4A) mRNA, partial sequence, alternatively spliced.
JD154795 - Sequence 135819 from Patent EP1572962.
JD299896 - Sequence 280920 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UMR7 (Reactome details) participates in the following event(s):

R-HSA-5621367 CLEC4A binds HIV and HCV glycoproteins
R-HSA-5621480 Dectin-2 family
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: CLC4A_HUMAN, CLECSF6, DCIR, HDCGC13P, LLIR, NM_016184, NP_057268, Q17R69, Q8WXW9, Q9H2Z9, Q9NS33, Q9UI34, Q9UMR7
UCSC ID: uc001qtz.1
RefSeq Accession: NM_016184
Protein: Q9UMR7 (aka CLC4A_HUMAN)
CCDS: CCDS8590.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016184.3
exon count: 6CDS single in 3' UTR: no RNA size: 1284
ORF size: 714CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1553.00frame shift in genome: no % Coverage: 99.77
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.